Polynucleotides encoding recombinant respiratory syncytial viruses expressing immune modulatory molecules

Abstract

Recombinant respiratory syncytial virus (RSV) are provided which express one or more immune modulatory molecules. The recombinant virus is modified by addition or substitution of a polynucleotide sequence encoding the immune modulatory molecule, which is preferably a cytokine. Introduction of the cytokine increase, decrease, or otherwise enhances aspects of viral biology and/or host immune responses to RSV to facilitate vaccine use of the virus. Cytokines for use within the invention include but are not limited to interleukin 2 (IL-2), interleukin 4 (IL-4), interleukin 5 (IL-5), interleukin 6 (IL6), or interleukin 18 (IL-18), tumor necrosis factor (TNF) alpha, interferon gamma (IFN), and granulocyte-macrophage colony stimulating factor (GM-CSF). The polynucleotide or immune modulatory molecule is preferably added or substituted into the recombinant viral genome or antigenome, typically at an intergenic or other non-coding site, as a separate gene but may be otherwise expressed, for example as a fusion protein.

1. An isolated polynucleotide molecule comprising a recombinant respiratory syncytial virus (RSV) genome or antigenome comprising polynucleotide sequences encoding a major nucleocapsid (N) protein, a nucleocapsid phosphoprotein (P), a large polymerase protein (L), and a M2(ORF1) polymerase elongation factor, and wherein said recombinant RSV genome or antigenome is modified to incorporate a heterologous polynucleotide sequence encoding an immune modulatory molecule selected from the group consisting of interleukin 2 (IL-2), interleukin 4 (IL-4), interferon gamma (IFNλ) and granulocyte-macrophage colony stimulating factor (GM-CSF), BlyS ligand, Flt3 and CD40. 
     
     
       2. The isolated polynucleotide molecule of  claim 1 , wherein the cytokine is interferon gamma (IFNλ). 
     
     
       3. The isolated polynucleotide molecule of  claim 1 , wherein the cytokine is granulocyte-macrophage colony stimulating factor (GM-CSF). 
     
     
       4. The isolated polynucleotide molecule of  claim 1 , wherein the cytokine is interleukin 2 (IL-2). 
     
     
       5. The isolated polynucleotide molecule of  claim 1 , wherein the cytokine is interleukin 4 (IL-4). 
     
     
       6. The isolated polynucleotide molecule of  claim 1 , wherein growth of a recombinant RSV encoded by said recombinant genome or antigenome in cell culture is attenuated by approximately 10-15 fold or greater compared to growth of a corresponding wild-type or mutant parental RSV strain. 
     
     
       7. The isolated polynucleotide molecule of  claim 1 , wherein a recombinant RSV encoded by said recombinant genome or antigenome expresses the immune modulatory molecule in cell culture medium at a level of between about 10-20 micrograms per 10 6  cells or greater. 
     
     
       8. The isolated polynucleotide molecule of  claim 1 , wherein a recombinant RSV encoded by said recombinant genome or antigenome is attenuated for growth in cell culture and for replication in both the upper and lower respiratory tracts of a mammalian host, and wherein the virus induces an immune response to RSV in an immunized host. 
     
     
       9. The isolated polynucleotide molecule of  claim 1 , wherein a recombinant RSV encoded by said recombinant genome or antigenome is attenuated by the activity of the immune modulatory molecule expressed in infected cells. 
     
     
       10. The isolated polynucleotide molecule of  claim 1 , wherein a recombinant RSV encoded by said recombinant genome or antigenome induces titers of serum IgG that are 2 to 10-fold higher or more than levels of serum IgG induced by wild type RSV. 
     
     
       11. The isolated polynucleotide molecule of  claim 1 , wherein the recombinant genome or antigenome incorporates one or more attenuating mutations from a human RSV. 
     
     
       12. The isolated polynucleotide molecule of  claim 11 , wherein the recombinant genome or antigenome incorporates at least one and up to a full complement of attenuating mutations present within a panel of mutant human RSV strains, said panel comprising cpts RSV 248 (ATCC VR 2450), cpts RSV 248/404 (ATCC VR 2454), cpts RSV 248/955 (ATCC VR 2453), cpts RSV 530 (ATCC VR 2452), cpts RSV 530/1009 (ATCC VR 2451), cpts RSV 530/1030 (ATCC VR 2455), RSV B-1 cp52/2B5 (ATCC VR 2542), and RSV B-1 cp-23 (ATCC VR 2579). 
     
     
       13. The isolated polynucleotide molecule of  claim 11 , wherein the recombinant genome or antigenome incorporates at least one and up to a full complement of attenuating mutations specifying an amino acid substitution at Val267 in the RSV N gene, Glu218 and/or Thr523 in the RSV F gene, Asn43, Cys319, Phe 521, Gln831, Met1169, Tyr1321 and/or His 1690 in the RSV polymerase gene L, and a nucleotide substitution in the gene-start sequence of gene M2. 
     
     
       14. The isolated polynucleotide molecule of  claim 11 , wherein the recombinant genome or antigenome incorporates at least two attenuating mutations. 
     
     
       15. The isolated polynucleotide molecule of  claim 11 , wherein the recombinant genome or antigenome includes at least one attenuating mutation stabilized by multiple nucleotide changes in a codon specifying the mutation. 
     
     
       16. The isolated polynucleotide molecule of  claim 1 , wherein the recombinant genome or antigenome incorporates a nucleotide modification specifying a phenotypic change selected from the group consisting of a change in growth in cell culture, attenuation, temperature-sensitivity, cold-adaptation, plaque size, host-range restriction, antigen expression and a change in immunogenicity. 
     
     
       17. The isolated polynucleotide molecule of  claim 16 , wherein the nucleotide modification specifying the phenotypic change alters a SH, NS1, NS2, M2 ORF2, or G gene of the recombinant RSV. 
     
     
       18. The isolated polynucleotide molecule of  claim 17 , wherein a SH, NS1, NS2, M2 ORF2, or G gene is deleted from said recombinant genome or antigenome in whole or in part or expression of the gene is reduced or ablated by a frame shift or introduction of one or more stop codons in an open reading frame of the gene or a modification of a translational start site. 
     
     
       19. The isolated polynucleotide molecule of  claim 16 , wherein the nucleotide modification specifying the phenotypic change comprises a nucleotide deletion, insertion, substitution, addition or rearrangement of a cis-acting regulatory sequence of a selected gene within the recombinant RSV genome or antigenome. 
     
     
       20. The isolated polynucleotide molecule of  claim 16 , wherein a gene end (GE) signal of the NS1 or NS2 gene is modified. 
     
     
       21. The isolated polynucleotide molecule of  claim 16 , wherein the nucleotide modification specifying the phenotypic change comprises an insertion, deletion, substitution, or rearrangement of a translational start site within the recombinant RSV genome or antigenome. 
     
     
       22. The isolated polynucleotide molecule of  claim 21 , wherein the translational start site for a secreted form of the RSV G glycoprotein is ablated. 
     
     
       23. The isolated polynucleotide molecule of  claim 16 , wherein the recombinant genome or antigenome is modified to encode a non-RSV molecule selected from the group consisting of one or more T-helper epitope(s), a restriction site marker, or a protein of a microbial pathogen capable of eliciting a protective immune response in a mammalian host. 
     
     
       24. The isolated polynucleotide molecule of  claim 16 , wherein the recombinant genome or antigenome incorporates a gene or genome segment from parainfluenza virus (PIV). 
     
     
       25. The isolated polynucleotide molecule of  claim 24 , wherein the gene or genome segment encodes a PIV HN or F glycoprotein or immunogenic domain or epitope thereof. 
     
     
       26. The isolated polynucleotide molecule of  claim 24 , wherein the genome segment encodes an ectodomain or immunogenic epitope of HN or F of PIV1, PIV2, or PIV3. 
     
     
       27. The isolated polynucleotide molecule of  claim 1 , wherein the recombinant genome or antigenome comprises a partial or complete RSV background genome or antigenome of a human or bovine RSV combined with a heterologous gene or genome segment of a different RSV to form a human-bovine chimeric RSV genome or antigenome. 
     
     
       28. The isolated polynucleotide molecule of  claim 27 , wherein the heterologous gene or genome segment encodes a RSV F, G or SH glycoprotein or an immunogenic domain or epitope thereof. 
     
     
       29. The isolated polynucleotide molecule of  claim 27 , wherein the heterologous gene or genome segment is substituted for a counterpart gene or genome segment in a partial RSV background genome or antigenome. 
     
     
       30. The isolated polynucleotide molecule of  claim 27 , wherein the heterologous gene or genome segment is added adjacent to or within a noncoding region of the partial or complete RSV background genome or antigenome. 
     
     
       31. The isolated polynucleotide molecule of  claim 27 , wherein the chimeric genome or antigenome comprises a partial or complete human RSV background genome or antigenome combined with a heterologous gene or genome segment from a bovine RSV. 
     
     
       32. The isolated polynucleotide molecule of  claim 27 , wherein the chimeric genome or antigenome comprises a partial or complete bovine RSV background genome or antigenome combined with a heterologous gene or genome segment from a human RSV. 
     
     
       33. The isolated polynucleotide molecule of  claim 32 , wherein one or more human RSV glycoprotein genes F, G and SH or a genome segment encoding a cytoplasmic domain, transmembrane domain, ectodomain or immunogenic epitope thereof is substituted for a counterpart gene or genome segment within the bovine RSV background genome or antigenome. 
     
     
       34. The isolated polynucleotide molecule of  claim 33 , wherein one or both human RSV glycoprotein genes F and G is substituted to replace one or both counterpart F and G glycoprotein genes in the bovine RSV background genome or antigenome. 
     
     
       35. The isolated polynucleotide molecule of  claim 34 , wherein both human RSV glycoprotein genes F and G are substituted to replace counterpart F and G glycoprotein genes in the bovine RSV background genome or antigenome. 
     
     
       36. The isolated polynucleotide molecule of  claim 35 , wherein the heterologous gene or genome segment is from a subgroup A or subgroup B human RSV. 
     
     
       37. The isolated polynucleotide molecule of  claim 35 , wherein the human-bovine chimeric genome or antigenome incorporates antigenic determinants from both subgroup A and subgroup B human RSV. 
     
     
       38. The isolated polynucleotide molecule of  claim 1 , wherein the recombinant genome or antigenome encodes a RSV that is a complete virus. 
     
     
       39. The isolated polynucleotide molecule of  claim 1 , wherein the recombinant genome or antigenome encodes a RSV that is a subviral particle. 
     
     
       40. The isolated polynucleotide molecule of  claim 1 , wherein the recombinant genome or antigenome comprises a partial or complete RSV vector genome or antigenome combined with one or more heterologous genes or genome segments encoding one or more antigenic determinants of one or more heterologous pathogens. 
     
     
       41. The isolated polynucleotide molecule of  claim 40 , wherein said one or more heterologous pathogens is a heterologous RSV and said heterologous gene(s) or genome segment(s) encode(s) one or more RSV NS1, NS2, N, P, M, SH, M2(ORF1), M2(ORF2), L, F or G protein(s) or fragment(s) thereof. 
     
     
       42. The isolated polynucleotide molecule of  claim 40 , wherein the vector genome or antigenome is a partial or complete RSV A genome or antigenome and the heterologous gene(s) or genome segment(s) encoding the antigenic determinant(s) is/are of a RSV B subgroup virus. 
     
     
       43. The isolated polynucleotide molecule of  claim 40 , wherein the chimeric genome or antigenome incorporates one or more gene(s) or genome segment(s) of a BRSV that specifies attenuation. 
     
     
       44. The isolated polynucleotide molecule of  claim 40 , wherein one or more HPIV1, HPIV2, or HPIV3 gene(s) or genome segment(s) encoding one or more HN and/or F glycoprotein(s) or antigenic domain(s), fragment(s) or epitope(s) thereof is/are added to or incorporated within the partial or complete HRSV vector genome or antigenome. 
     
     
       45. The isolated polynucleotide molecule of  claim 40 , wherein the vector genome or antigenome is a partial or complete BRSV genome or antigenome and the heterologous gene(s) or genome segment(s) encoding the antigenic determinant(s) is/are of one or more HRSV(s). 
     
     
       46. The isolated polynucleotide molecule of  claim 45 , wherein the partial or complete BRSV genome or antigenome incorporates one or more gene(s) or genome segment(s) encoding one or more HRSV glycoprotein genes selected from the group consisting of F, G and SH and one or more genome segment(s) encoding cytoplasmic domain, transmembrane domain, ectodomain or immunogenic epitope portion(s) of F, G, and SH of HRSV. 
     
     
       47. The isolated polynucleotide molecule of  claim 40 , wherein the vector genome or antigenome is a partial or complete HRSV or BRSV genome or antigenome and the heterologous pathogen is selected from the group consisting of measles virus, subgroup A and subgroup B respiratory syncytial viruses, mumps virus, human papilloma viruses, type 1 and type 2 human immunodeficiency viruses, herpes simplex viruses, cytomegalovirus, rabies virus, Epstein Barr virus, filoviruses, bunyaviruses, flaviviruses, alphaviruses and influenza viruses. 
     
     
       48. The isolated polynucleotide molecule of  claim 47 , wherein said one or more heterologous antigenic determinant(s) is/are selected from the group consisting of measles virus HA and F proteins, subgroup A or subgroup B respiratory syncytial virus F, G, SH and M2 proteins, mumps virus HN and F proteins, human papilloma virus L1 protein, type 1 or type 2 human immunodeficiency virus gp160 protein, herpes simplex virus and cytomegalovirus gB, gC, gD, gE, gG, gH, gI, gJ, gK, gL, and gM proteins, rabies virus G protein, Epstein Barr Virus gp350 protein; filovirus G protein, bunyavirus G protein, Flavivirus E and NS1 proteins, and alphavirus B protein, and antigenic domains, fragments and epitopes thereof. 
     
     
       49. The isolated polynucleotide molecule of  claim 47 , wherein the heterologous pathogen is measles virus and the heterologous antigenic determinant(s) is/are selected from the group consisting of the measles virus HA and F proteins, and antigenic domains, fragments and epitopes thereof. 
     
     
       50. The isolated polynucleotide molecule of  claim 49 , wherein a transcription unit comprising an open reading frame (ORF) of a measles virus HA gene is added to or incorporated within a HRSV vector genome or antigenome. 
     
     
       51. The isolated polynucleotide molecule of  claim 1 , wherein the recombinant genome or antigenome has one or more shifted RSV gene(s) or genome segment(s) within said recombinant genome or antigenome that is/are positionally shifted to a more promoter-proximal or promoter-distal position relative to a position of said RSV gene(s) or genome segment(s) within a wild type RSV genome or antigenome. 
     
     
       52. The isolated polynucleotide molecule of  claim 51 , wherein said one or more shifted gene(s) or genome segment(s) is/are shifted to a more promoter-proximal or promoter-distal position by deletion, insertion or rearrangement of one or more displacement polynucleotide(s) within said partial or complete recombinant RSV genome or antigenome. 
     
     
       53. The isolated polynucleotide molecule of  claim 52 , wherein said displacement polynucleotide(s) comprise(s) one or more polynucleotide insert(s) of between 150 nucleotides (nts) and 4,000 nucleotides in length which is inserted in a non-coding region (NCR) of the genome or antigenome or as a separate gene unit (GU), said polynucleotide insert lacking a complete open reading frame (ORF) and specifying an attenuated phenotype in said recombinant RSV. 
     
     
       54. The isolated polynucleotide molecule of  claim 52 , wherein said displacement polynucleotide(s) comprise(s) one or more RSV gene(s) or genome segment(s) selected from the group consisting of RSV NS1, NS2, N, P, M, SH, M2(ORF1), M2(ORF2), L, F and G genes and genome segments thereof and leader, trailer and intergenic regions of the RSV genome and segments thereof. 
     
     
       55. The isolated polynucleotide molecule of  claim 52 , wherein said displacement polynucleotide(s) comprise(s) one or more bovine RSV (BRSV) or human RSV (HRSV) gene(s) or genome segment(s) selected from RSV NS1, NS2, N, P, M, SH, M2(ORF1), M2(ORF2), L, F and G gene(s) or genome segment(s) and leader, trailer and intergenic regions of the RSV genome or segments thereof. 
     
     
       56. The isolated polynucleotide molecule of  claim 55 , wherein said displacement polynucleotide(s) is/are deleted to form the recombinant RSV genome or antigenome to cause a positional shift of said one or more shifted RSV gene(s) or genome segment(s) within said recombinant genome or antigenome to a more promoter-proximal position relative to a position of said RSV gene(s) or genome segment(s) within a wild type RSV genome or antigenome. 
     
     
       57. The isolated polynucleotide molecule of  claim 56 , wherein said displacement polynucleotide(s) that is/are deleted to form the recombinant RSV genome or antigenome comprise one or more RSV NS1, NS2, SH, M2(ORF2), or G gene(s) or genome segment(s) thereof. 
     
     
       58. The isolated polynucleotide molecule of  claim 51 , wherein the RSV glycoprotein gene G is rearranged within said recombinant RSV genome or antigenome to a gene order position that is more promoter-proximal compared to the wild type gene order position of G. 
     
     
       59. The isolated polynucleotide molecule of  claim 51 , wherein the RSV glycoprotein gene F is rearranged within said recombinant RSV genome or antigenome to a gene order position that is more promoter-proximal compared to the wild type gene order position of F. 
     
     
       60. The isolated polynucleotide molecule of  claim 51 , wherein both RSV glycoprotein genes G and F are rearranged within said recombinant RSV genome or antigenome to gene order positions that are more promoter-proximal compared to the wild type gene order positions of G and F. 
     
     
       61. The isolated polynucleotide molecule of  claim 60 , wherein the RSV glycoprotein gene G is shifted to gene order position 1 and the RSV glycoprotein gene F is shifted to gene order position 2 within said recombinant RSV genome or antigenome. 
     
     
       62. The isolated polynucleotide molecule of  claim 51 , wherein the RSV SH and NS2 genes are both deleted to form the recombinant RSV genome. 
     
     
       63. The isolated polynucleotide molecule of  claim 51 , wherein the RSV SH, NS1 and NS2 genes are all deleted to form the recombinant RSV genome.